DOCSLIB.ORG

Variability of Rrna Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Variability of Rrna Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem ORIGINAL RESEARCH published: 05 January 2016 doi: 10.3389/fmicb.2015.01486 Variability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem Jorge A. Valdivia-Anistro1, Luis E. Eguiarte-Fruns1, Gabriela Delgado-Sapién2, Pedro Márquez-Zacarías3, Jaime Gasca-Pineda1, Jennifer Learned4, James J. Elser4, Gabriela Olmedo-Alvarez5 and Valeria Souza1* 1 Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Mexico, 2 Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, Mexico, 3 School of Biology, Georgia Institute of Technology, Atlanta, GA, USA, 4 School of Life Sciences, Arizona State University, Tempe, AZ, USA, 5 Laboratorio de Bacteriología Molecular, Departamento de Ingeniería Genética, CINVESTAV – Unidad Irapuato, Irapuato, Mexico The ribosomal RNA (rrn) operon is a key suite of genes related to the production Edited by: of protein synthesis machinery and thus to bacterial growth physiology. Experimental Roland Hatzenpichler, evidence has suggested an intrinsic relationship between the number of copies of this California Institute of Technology, USA operon and environmental resource availability, especially the availability of phosphorus Reviewed by: (P), because bacteria that live in oligotrophic ecosystems usually have few rrn operons Sebastian Kopf, Princeton University, USA and a slow growth rate. The Cuatro Ciénegas Basin (CCB) is a complex aquatic Albert Leopold Mueller, ecosystem that contains an unusually high microbial diversity that is able to persist Stanford University, USA under highly oligotrophic conditions. These environmental conditions impose a variety *Correspondence: Valeria Souza of strong selective pressures that shape the genome dynamics of their inhabitants. The [email protected] genus Bacillus is one of the most abundant cultivable bacterial groups in the CCB and usually possesses a relatively large number of rrn operon copies (6–15 copies). The Specialty section: This article was submitted to main goal of this study was to analyze the variation in the number of rrn operon copies Microbial Physiology and Metabolism, of Bacillus in the CCB and to assess their growth-related properties as well as their a section of the journal Frontiers in Microbiology stoichiometric balance (N and P content). We defined 18 phylogenetic groups within the Received: 16 September 2015 Bacilli clade and documented a range of from six to 14 copies of the rrn operon. The Accepted: 09 December 2015 growth dynamic of these Bacilli was heterogeneous and did not show a direct relation Published: 05 January 2016 to the number of operon copies. Physiologically, our results were not consistent with Citation: the Growth Rate Hypothesis, since the copies of the rrn operon were decoupled from Valdivia-Anistro JA, Eguiarte-Fruns LE, growth rate. However, we speculate that the diversity of the growth properties of these Delgado-Sapién G, Bacilli as well as the low P content of their cells in an ample range of rrn copy number Márquez-Zacarías P, Gasca-Pineda J, Learned J, Elser JJ, is an adaptive response to oligotrophy of the CCB and could represent an ecological Olmedo-Alvarez G and Souza V mechanism that allows these taxa to coexist. These findings increase the knowledge (2016) Variability of rRNA Operon of the variability in the number of copies of the rrn operon in the genus Bacillus and Copy Number and Growth Rate Dynamics of Bacillus Isolated from an give insights about the physiology of this bacterial group under extreme oligotrophic Extremely Oligotrophic Aquatic conditions. Ecosystem. Front. Microbiol. 6:1486. doi: 10.3389/fmicb.2015.01486 Keywords: rRNA operon copies, oligotrophy, bacterial growth, Bacillus, Cuatro Ciénegas Frontiers in Microbiology | www.frontiersin.org 1 January 2016 | Volume 6 | Article 1486 Valdivia-Anistro et al. rrn Operon and Growth Dynamics INTRODUCTION copy number may be favored because the rich P supply could then support the rapid production of P-rich rrn to meet the Population genetics is the most direct tool for use in protein demands of rapid growth, as stated by the “Growth understanding adaptation to the ecological challenges imposed Rate Hypothesis” (GRH), a core idea within the theory of upon microbial communities by the environment (Whitaker biological stoichiometry (Elser et al., 2000; Elser, 2006). However, et al., 2003; Xu, 2006; Spencer et al., 2008). Functional traits can in environments with low phosphorus availability, multiple aid in the study of population genetics, because they help to define rrn operon copies could represent a competitive cost if a species in terms of their ecological roles, such as how they use high rrn operon copy number leads to the over-production environmental resources or how they interact with other species of P-rich rrn (Sterner and Elser, 2002; Maciá, 2005; Jeyasingh (McGill et al., 2006; Hughes et al., 2008). These functional traits and Weider, 2007). Indeed, aquatic bacteria isolated from are often considered to be ecological strategies because they are oligotrophic environments usually have low rrn operon copy useful in understanding why certain bacteria live in a particular numbers (Fegatella et al., 1998; Strehl et al., 1999; Lauro et al., environment and how they respond to environmental challenges 2009), as well as various other adaptations to decrease cellular (Green et al., 2008). phosphorus demand (Cavicchioli et al., 2003; Alcaraz et al., The ribosomal RNA operon (rrn hereafter) is the key genetic 2008; Martiny et al., 2009; Van Mooy et al., 2009). Thus, it has structure for protein synthesis and thus a functional trait been proposed that there is a connection between the number related to bacterial life history (Stevenson and Schmidt, 2004). of rrn operon copies and environmental P availability (Elser Ecologically, the rrn operon has been related with the bacterial et al., 2000; Weider et al., 2005; Jeyasingh and Weider, 2007). capacity to respond to changes in environmental conditions However, to our knowledge, we lack extensive studies that (Codon et al., 1995; Prüβ et al., 1999; Green et al., 2008). In document this variation in rrn operon copy number and other particular, the variation in the number of copies of the rrn associated ecological strategies employed by bacteria coexisting operon has been considered an ecological strategy related to in oligotrophic environments, especially those characterized by resource availability, with physiological implications associated severe P limitation. with bacterial growth rate and fitness (Klappenbach et al., 2000; The aims of this study were to describe rrn operon Shrestha et al., 2007). The rrn operon is comprised of three genes copy number variation in different lineages of Bacillus strains (5S, 16S, and 23S rDNA) and its copy number varies from 1 to isolated from an extremely oligotrophic ecosystem and to 15 among bacterial genomes (Klappenbach et al., 2001; Acinas analyze the possible association between the copy number and et al., 2004; Stoddard et al., 2015) and even more dramatically its physiological implications for growth rate and chemical among eukaryotes (Elser et al., 2000). Experimentally, it has been composition (P content and N:P stoichiometry). Severe P shown that deletions of one or more copies of the rrn operon limitation is considered a primary selective pressure that drives have a considerable impact on growth rate, affecting various bacterial evolution in this environment (Souza et al., 2008, 2012). stress-response mechanisms (Nanamiya et al., 2010; Yano et al., For example, we have previously reported on an endemic and 2013). Hence, it has been suggested that the multiplicity of the moderately halophilic Bacillus (type strain of B. coahuilensis: rrn operon is a potential mechanism for adaptation to different m4-4 = NRRL B-41737T), (Cerritos et al., 2008)thathasa environmental conditions (Elser et al., 2000; Green et al., 2008). typical number of rrn copies (nine) but also clear adaptations to In general terms, bacteria that possess more rrn operon copies the extreme oligotrophic conditions, including a small genome may cope better with fluctuating nutrient inputs than bacteria (3.5 Mb), a diversity of phosphate acquisition genes (Moreno- with fewer rrn operon copies, which tend to live in environments Letelier et al., 2011), and a cellular membrane composed of where nutrients are scarce (Klappenbach et al., 2001; Elser, 2003; sulfolipids (Alcaraz et al., 2008). Similar adaptations to low Jeyasingh and Weider, 2007). Moreover, the relationship between P levels have been reported only from oligotrophic marine rrn operon copy number and the bacterial biotic potential for cyanobacteria with low rrn copy numbers (Cavicchioli et al., the cellular allocation of key resources could be analogous to 2003; Lauro et al., 2009; Martiny et al., 2009; Van Mooy et al., the ecological strategies described in other macro-biota (r- and 2009). Hence, the present study represents the first attempt to link K-strategies), (Pianka, 1970; Elser et al., 2000; Dethlefsen and biological stoichiometry to Bacillus diversity and rrn operon copy Schmidt, 2007; Shrestha et al., 2007; Lipowsky et al., 2012). number, as well as the first report in which the numbers of rrn Bacillus is a genus that is well-known because of its copies are analyzed
Load more

Recommended publications
  • Research Article Genomic Analysis of Bacillus Megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil
    Hindawi International Journal of Genomics Volume 2020, Article ID 4109186, 11 pages https://doi.org/10.1155/2020/4109186 Research Article Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil Bin Wang ,1 Dan Zhang,1 Shaohua Chu ,1 Yuee Zhi,1 Xiaorui Liu ,2 and Pei Zhou 1 1School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China 2The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China Correspondence should be addressed to Xiaorui Liu; [email protected] and Pei Zhou; [email protected] Received 11 November 2019; Revised 1 February 2020; Accepted 8 February 2020; Published 29 February 2020 Guest Editor: Ravi Kant Copyright © 2020 Bin Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate- solubilizing ability, and Trp-dependent IAA synthetic system.
    [Show full text]
  • Bacillus Crassostreae Sp. Nov., Isolated from an Oyster (Crassostrea Hongkongensis)
    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1561–1566 DOI 10.1099/ijs.0.000139 Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis) Jin-Hua Chen,1,2 Xiang-Rong Tian,2 Ying Ruan,1 Ling-Ling Yang,3 Ze-Qiang He,2 Shu-Kun Tang,3 Wen-Jun Li,3 Huazhong Shi4 and Yi-Guang Chen2 Correspondence 1Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Yi-Guang Chen Hunan Agricultural University, 410128 Changsha, PR China [email protected] 2College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China 3The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China 4Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 6C (optimum 30–35 6C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0,C16 : 0 and C16 : 1v11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%.
    [Show full text]
  • Identification and Sequence Analyses of Novel Lipase Encoding Novel
    Shahinyan et al. BMC Microbiology (2017) 17:103 DOI 10.1186/s12866-017-1016-4 RESEARCH ARTICLE Open Access Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs Grigor Shahinyan1, Armine Margaryan1,2, Hovik Panosyan2 and Armen Trchounian1,2* Abstract Background: Among the huge diversity of thermophilic bacteria mainly bacilli have been reported as active thermostable lipase producers. Geothermal springs serve as the main source for isolation of thermostable lipase producing bacilli. Thermostable lipolytic enzymes, functioning in the harsh conditions, have promising applications in processing of organic chemicals, detergent formulation, synthesis of biosurfactants, pharmaceutical processing etc. Results: In order to study the distribution of lipase-producing thermophilic bacilli and their specific lipase protein primary structures, three lipase producers from different genera were isolated from mesothermal (27.5–70 °C) springs distributed on the territory of Armenia and Nagorno Karabakh. Based on phenotypic characteristics and 16S rRNA gene sequencing the isolates were identified as Geobacillus sp., Bacillus licheniformis and Anoxibacillus flavithermus strains. The lipase genes of isolates were sequenced by using initially designed primer sets. Multiple alignments generated from primary structures of the lipase proteins and annotated lipase protein sequences, conserved regions analysis and amino acid composition have illustrated the similarity (98–99%) of the lipases with true lipases (family I) and GDSL esterase family (family II). A conserved sequence block that determines the thermostability has been identified in the multiple alignments of the lipase proteins. Conclusions: The results are spreading light on the lipase producing bacilli distribution in geothermal springs in Armenia and Nagorno Karabakh.
    [Show full text]
  • Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile
    Hindawi International Journal of Microbiology Volume 2018, Article ID 4375164, 7 pages https://doi.org/10.1155/2018/4375164 Research Article Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile Noha Ahmed Abd Alfadil ,1 Malik Suliman Mohamed ,2 Manal M. Ali,3 and El Amin Ibrahim El Nima2 1Department of Pharmaceutics, Faculty of Pharmacy, University of Al Neelain, Khartoum, Sudan 2Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan 3Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Omdurman Islamic University, Khartoum, Sudan Correspondence should be addressed to Noha Ahmed Abd Alfadil; [email protected] Received 18 May 2018; Revised 16 July 2018; Accepted 8 August 2018; Published 24 September 2018 Academic Editor: Susana Merino Copyright © 2018 Noha Ahmed Abd Alfadil et al. (is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. Banknotes are one of the most exchangeable items in communities and always subject to contamination by pathogenic bacteria and hence could serve as vehicle for transmission of infectious diseases. (is study was conducted to assess the prevalence of contamination by pathogenic bacteria in Sudanese banknotes, determine the susceptibility of the isolated organisms towards commonly used antibiotics, and detect some antibiotic resistance genes. Methods. (is study was carried out using 135 samples of Sudanese banknotes of five different denominations (2, 5, 10, 20, and 50 Sudanese pounds), which were collected randomly from hospitals, food sellers, and transporters in all three districts of Khartoum, Bahri, and Omdurman.
    [Show full text]
  • Biochemical Characterization and 16S Rdna Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com ScienceDirect IERI Procedia 5 ( 2013 ) 258 – 264 2013 International Conference on Agricultural and Natural Resources Engineering Biochemical Characterization and 16S rDNA Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia a a a a M.J., Norashirene , H., Umi Sarah , M.H, Siti Khairiyah and S., Nurdiana aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia. Abstract Thermophiles are well known as organisms that can withstand extreme temperature. Thermoenzymes from thermophiles have numerous potential for biotechnological applications due to their integral stability to tolerate extreme pH and elevated temperature. Because of the industrial importance of lipases, there is ongoing interest in the isolation of new bacterial strain producing lipases. Six isolates of lipases producing thermophiles namely K7S1T53D5, K7S1T53D6, K7S1T53D11, K7S1T53D12, K7S2T51D14 and K7S2T51D19 were isolated from the Selayang Hot Spring, Malaysia. The sampling site is neutral in pH with a highest recorded temperature of 53°C. For the screening and isolation of lipolytic thermopiles, selective medium containing Tween 80 was used. Thermostability and the ability to degrade the substrate even at higher temperature was proved and determined by incubation of the positive isolates at temperature 53°C. Colonies with circular borders, convex in elevation with an entire margin and opaque were obtained. 16S rDNA gene amplification and sequence analysis were done for bacterial identification. The isolate of K7S1T53D6 was derived of genus Bacillus that is the spore forming type, rod shaped, aerobic, with the ability to degrade lipid.
    [Show full text]
  • The Genome of Bacillus Coahuilensis Reveals Adaptations Essential for Survival in the Relic of an Ancient Marine Environment
    The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment Luis David Alcaraz*, Gabriela Olmedo*, Germa´ n Bonilla†, Rene´ Cerritos†, Gustavo Herna´ ndez‡, Alfredo Cruz‡, Enrique Ramı´rez§, Catherine Putonti¶, Beatriz Jime´nez*‡, Eva Martı´nez*,Varinia Lo´pez*, Jacqueline L. Arvizu*, Francisco Ayala*, Francisco Razo*, Juan Caballero*, Janet Siefertʈ, Luis Eguiarte†, Jean-Philippe Vielle*‡, Octavio Martı´nez*‡, Valeria Souza†, Alfredo Herrera-Estrella*‡, and Luis Herrera-Estrella*‡** ‡Laboratorio Nacional de Geno´mica para la Biodiversidad (Langebio), *Departamento de Ingenierı´aGene´tica and §Departamento de Biotecnologı´a, Cinvestav, Campus Guanajuato, AP 629 Irapuato, Guanajuato CP36500, Me´xico; †Departamento de Ecologı´aEvolutiva, Instituto de Ecologı´a,Universidad Nacional Auto´noma de Me´xico, CU, AP 70-275 Coyoaca´n 04510 Me´xico D.F., Me´xico; ʈDepartment of Statistics, Rice University, P.O. Box 1892, MS-138, Houston, TX 77251-1892; and ¶Departments of Computer Science and Biology and Biochemistry, 4800 Cullen Boulevard, University of Houston, Houston, TX 77204-5001 Contributed by Luis Herrera-Estrella, January 31, 2008 (sent for review December 10, 2007) The Cuatro Cie´negas Basin (CCB) in the central part of the Chihua- phylogenetic analysis of 16S rRNA sequences indicates that B. han desert (Coahuila, Mexico) hosts a wide diversity of microor- coahuilensis is closely related to other marine Bacillus spp. (4), in ganisms contained within springs thought to be geomorphological agreement with the theory of an ancient marine origin of these relics of an ancient sea. A major question remaining to be answered ponds. We sequenced the genome of B.
    [Show full text]
  • Molecular Diversity and Multifarious Plant Growth
    Environment Health Techniques 44 Priyanka Verma et al. Research Paper Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India Priyanka Verma1,2, Ajar Nath Yadav1, Kazy Sufia Khannam2, Sanjay Kumar3, Anil Kumar Saxena1 and Archna Suman1 1 Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India 2 Department of Biotechnology, National Institute of Technology, Durgapur, India 3 Division of Genetics, Indian Agricultural Research Institute, New Delhi, India The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19–27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, andStaphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia).
    [Show full text]
  • Genomics of Bacteria from an Ancient Marine Origin: Clues to Survival in an Oligotrophic Environment
    26 Genomics of Bacteria from an Ancient Marine Origin: Clues to Survival in an Oligotrophic Environment Luis David Alcaraz1, Varinia López-Ramírez2, Alejandra Moreno-Letelier3, Luis Herrera-Estrella4, Valeria Souza5 and Gabriela Olmedo-Alvarez2 1Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, 2Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, 3Division of Biology, Imperial College London, Silwood Park Campus, Ascot, 4Langebio, Cinvestav, Mexico 5Departamento de Ecologia Evolutiva, Instituto de Ecologia, Universidad Nacional Autónoma de México 1Spain 2,4.5Mexico 3UK 1. Introduction Genomics Has certainly cHanged tHe way tHat biology is studied, and Has Had a substantial impact on many other scientific disciplines as well. Life and Earth have had an interdependent history since the early establishment of the biogeochemical cycles in tHe Archean. Genomic sequences provide historical information that can be correlated with tHe geological record. Thus, it is not surprising that comparative genomics aids in understanding current findings in geological sciences. Genomics allows us to explain tHe evolutionary History of an organism by analyzing and comparing tHe set of sHared genes with all respective relatives. Additionally, by examining the genes that are unique to some strains or taxonomic groups, we can make inferences about tHeir ecology. Since molecular biology was initially developed in bacterial model organisms and we have extensive knowledge about tHe enzymes tHat participate in different biocHemical patHways, inferences and functional predictions can be made about numerous sequenced genes. Moreover, due to the energetic and evolutionary costs of preserving a gene in bacteria, where specialists tend to have small size genomes, unique genes may aid in exploiting a given niche.
    [Show full text]
  • Diversity of Cultivated Aerobic Poly-Hydrolytic Bacteria in Saline Alkaline Soils
    Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils Dimitry Y. Sorokin1,2, Tatiana V. Kolganova3, Tatiana V. Khijniak1, Brian E. Jones4 and Ilya V. Kublanov1,5 1 Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia 2 Department of Biotechnology, Delft University of Technology, Delft, Netherlands 3 Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia 4 DuPont Industrial Biosciences/Genencor International BV, Leiden, Netherlands 5 Immanuel Kant Baltic Federal University, Kaliningrad, Russia ABSTRACT Alkaline saline soils, known also as ``soda solonchaks'', represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic Submitted 9 June 2017 bacterial community in soda soils which might be explored further for production of Accepted 21 August 2017 haloalkalistable hydrolases.
    [Show full text]
  • Patterns of Horizontal Gene Transfer Into the Geobacillus Clade
    Imperial College London London Institute of Medical Sciences Patterns of Horizontal Gene Transfer into the Geobacillus Clade Alexander Dmitriyevich Esin September 2018 Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy of Imperial College London For my grandmother, Marina. Without you I would have never been on this path. Your unwavering strength, love, and fierce intellect inspired me from childhood and your memory will always be with me. 2 Declaration I declare that the work presented in this submission has been undertaken by me, including all analyses performed. To the best of my knowledge it contains no material previously published or presented by others, nor material which has been accepted for any other degree of any university or other institute of higher learning, except where due acknowledgement is made in the text. 3 The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 4 Abstract Horizontal gene transfer (HGT) is the major driver behind rapid bacterial adaptation to a host of diverse environments and conditions. Successful HGT is dependent on overcoming a number of barriers on transfer to a new host, one of which is adhering to the adaptive architecture of the recipient genome.
    [Show full text]
  • Microevolution Analysis of Bacillus Coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation
    ORIGINAL RESEARCH published: 08 February 2016 doi: 10.3389/fmicb.2016.00058 Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation Zulema Gómez-Lunar1, Ismael Hernández-González1, María-Dolores Rodríguez-Torres1, Valeria Souza2 and Gabriela Olmedo-Álvarez1* 1 Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico, 2 Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México City, Mexico Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was Edited by: to compare the genomes and relevant phenotypes of three Bacillus coahuilensis Frank T. Robb, strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin University of Maryland School (México), to unveil the environmental challenges that this species cope with, and the of Medicine, USA Reviewed by: microevolutionary differences in these genotypes. Since the strains were isolated from David John Studholme, a low P environment, we placed emphasis on the search of different phosphorus University of Exeter, UK acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of Juan M. Gonzalez, Consejo Superior de Investigaciones coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% Científicas, Spain corresponded to accessory genes. Most of the genes in this last group were associated *Correspondence: with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten Gabriela Olmedo-Álvarez percent of the pangenome consisted of strain-specific genes.
    [Show full text]
  • Manganese-II Oxidation and Copper-II Resistance in Endospore Forming Firmicutes Isolated from Uncontaminated Environmental Sites
    AIMS Environmental Science, 3(2): 220-238. DOI: 10.3934/environsci.2016.2.220 Received 21 January 2016, Accepted 05 April 2016, Published 12 April 2016 http://www.aimspress.com/journal/environmental Research article Manganese-II oxidation and Copper-II resistance in endospore forming Firmicutes isolated from uncontaminated environmental sites Ganesan Sathiyanarayanan 1,†, Sevasti Filippidou 1,†, Thomas Junier 1,2, Patricio Muñoz Rufatt 1, Nicole Jeanneret 1, Tina Wunderlin 1, Nathalie Sieber 1, Cristina Dorador 3 and Pilar Junier 1,* 1 Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Emile-Argand 11, CH-2000 Neuchâtel, Switzerland 2 Vital-IT group, Swiss Institute of Bioinformatics, CH-1000 Lausanne, Switzerland 3 Laboratorio de Complejidad Microbiana y Ecología Funcional; Departamento de Biotecnología; Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta; CL-, 1270190, Antofagasta, Chile * Correspondence: Email: [email protected]; Tel: +41-32-718-2244; Fax: +41-32-718-3001. † These authors contributed equally to this work. Abstract: The accumulation of metals in natural environments is a growing concern of modern societies since they constitute persistent, non-degradable contaminants. Microorganisms are involved in redox processes and participate to the biogeochemical cycling of metals. Some endospore-forming Firmicutes (EFF) are known to oxidize and reduce specific metals and have been isolated from metal-contaminated sites. However, whether EFF isolated from uncontaminated sites have the same capabilities has not been thoroughly studied. In this study, we measured manganese oxidation and copper resistance of aerobic EFF from uncontaminated sites. For the purposes of this study we have sampled 22 natural habitats and isolated 109 EFF strains.
    [Show full text]